Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1

Guillaume Gaullier; Genevieve Roberts; Uma M. Muthurajan; Samuel Bowerman; Johannes Rudolph; Jyothi Mahadevan; Asmita Jha; Purushka S. Rae; Karolin Luger

doi:10.1371/journal.pone.0240932

Peer Review History

Original SubmissionAugust 7, 2020
14 Sep 2020 Decision Letter - Robert W Sobol, Editor PONE-D-20-24696 Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1 PLOS ONE Dear Dr. Luger, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. As can be seen in the reviewer comments, there are several small but important points that are best addressed. I would hope that the authors can address the concerns raised by both reviewers. Please submit your revised manuscript by Oct 29 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. 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Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. 4. Please include your tables as part of your main manuscript and remove the individual files. Please note that supplementary tables (should remain/ be uploaded) as separate "supporting information" files. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: This is a well-written and interesting manuscript using a combination of in vitro biophysical tools to probe the interactions between PARP2, HPF1 and nucleosomes. A few minor comments are below. It would be nice to note how the PARP2-QFRD mutant was serendipitously discovered. In figure 1B, the dimerization of the nucleosome particles suggested by the authors, is not immediately apparent from the figure. The subsequent SEC-MALS analyses are more convincing than the figure displayed in 1B. In fig. 1D, are residues R140 and W138/ Y188 displayed? If these residues are displayed to highlight conservation, it would be nicer to see them in the context of a sequence alignment as well. Are they conserved through multiple species from bacteria, archaea to mammalian species? Also, these conserved residues were not discussed in the text (only in one of the figure legends). Why these specific residues were selected for display of conservation is not discussed. For Figure 2, Coomassie stained gels displaying the proteins/complexes would help clarify that both proteins are indeed present in the eluting fractions and clarify some of the ambiguity seen in the MW of each eluting species. Reviewer #2: Review of PONE-D-20-24696: The enzyme poly(ADP-ribose) polymerase-1 (PARP1), and the related enzyme PARP2, promote single- and double-strand DNA break repair in cells, by facilitating the local remodeling of chromatin into a repair-permissive configuration. PARP inhibitors suppress the repair of DNA damaged by radio- or chemotherapy, making them valuable in cancer therapy. This naturally has spurred efforts to better understand how the PARP enzymes function in chromatin. This manuscript presents the first cryo-EM structure of PARP2 bound to a DNA end near the edge of a nucleosome. The data throughout appear very solid, the interpretations are consistent with previous studies of PARP-2 structure and function, and the methods are clearly and thoroughly described. As such, I think this study will meaningfully advance the field. My only substantive comment relates to how PARP2 drives formation of the ‘di-nucleosomes’ used for structural analyses. At appropriate concentrations, the capacity of PARP2 to dimerize drove formation of di-nucleosomes, in which two PARP-2 molecules serve to bridge the DNA ends of two previously separate nucleosomes. The resulting complex (i.e. one PARP2 dimer and two nucleosomes) appears surprisingly homogeneous, as if the two nucleosomes were rotationally constrained relative to one another. One is tempted to attribute this homogeneity to the PARP2 dimer but, as the authors note, they cannot rule out stabilization through interactions between histone tails in one nucleosome and DNA in the adjacent nucleosome. Unfortunately, only the WGR-domain of PARP2 was amenable to structural analyses in this study. Previous X-ray crystallographic studies (PMID: 30321391) indicate that the WGR domain interacts with a 5’-phosphate at the break. However, that domain does not mediate dimer formation. Thus, while it seems highly likely that PARP2 contributes to di-nucleosome formation, it remains unclear if inter-nucleosome interactions between histones and DNA contribute as well. If such interactions occur, they would presumably be suppressed by the acetylation of histone tails in the model nucleosomes. Knowing how back-breakingly laborious cryo-EM studies can be, I don’t see this control experiment as obligatory but, ultimately, it might prove worthwhile. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. 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Revision 1
20 Sep 2020 Author Response We thank the reviewers for their insightful comments. Below is our response to each of the reviewer’s points. We have also addressed editorial issues and we hope that this manuscript is now suitable for publication in Plos1. • All raw images have been deposited in Zenodo at https://doi.org/10.5281/zenodo.3519436 • We have removed the ‘data not shown’ reference, as this is not a core part of the research presented. Reviewer #1: This is a well-written and interesting manuscript using a combination of in vitro biophysical tools to probe the interactions between PARP2, HPF1 and nucleosomes. A few minor comments are below. It would be nice to note how the PARP2-QFRD mutant was serendipitously discovered. The PARP2-QFRD mutant was designed based on HDX-MS data showing protection of a peptide encompassing residues Q112 and F113 of PARP2 when mixed with PARP1, compared to PARP2 by itself. We designed the mutations to be solvent-exposed and to change drastically the properties of amino acids at these positions while not changing the protein’s isoelectric point. We edited the manuscript to explain this on page 4. In figure 1B, the dimerization of the nucleosome particles suggested by the authors, is not immediately apparent from the figure. The subsequent SEC-MALS analyses are more convincing than the figure displayed in 1B. We added a cartoon depiction to make our interpretation of the micrographs more explicit. In fig. 1D, are residues R140 and W138/ Y188 displayed? If these residues are displayed to highlight conservation, it would be nicer to see them in the context of a sequence alignment as well. Are they conserved through multiple species from bacteria, archaea to mammalian species? Also, these conserved residues were not discussed in the text (only in one of the figure legends). Why these specific residues were selected for display of conservation is not discussed. Residues W138, R140 and Y188 are not shown in figure 1D. We assume the reviewer is referring to figure S1K, to which we added the sequence alignment that was used to color the structure by conservation. The sequences used for this conservation analysis are listed in supplementary information, but we agree with the reviewer that sequence identifiers alone are not enough information, so we added to this list the species these sequences originate from. All of the PARP2 orthologues and paralogues used in this analysis are from eukaryotes, covering animals, plants and fungi (bacteria and archaea don’t have PARP enzymes). We have included an exhaustive alignment to indicate that the residues Q112, F113 are variable across species. The W138, G139 (the latter not visible in stick representation because Gly has no side chain) and R140 residues form the WGR motif that is highly conserved in DNA-dependent PARP enzymes and after which the WGR domain is named. These are denoted in the alignments as the “WGR domain”. The Y188 residue makes a key protein-DNA interaction with the terminal 5’-phosphate at a DNA break (which is an essential part of break recognition, see PMID 30321391 and PDB 6F5B) and is also highly conserved. The Y188 residue is also indicated with an arrow in the alignments. We chose to display these conserved residues to contrast with residues 112 and 113 that are not particularly conserved and to make the point that the mutations Q112R and F113D are therefore not likely to perturb the protein beyond the self-association effect we observed with the wild type protein (figures 1A, 1B and S1A). We edited the manuscript to clarify this point. For Figure 2, Coomassie stained gels displaying the proteins/complexes would help clarify that both proteins are indeed present in the eluting fractions and clarify some of the ambiguity seen in the MW of each eluting species. We do not have an SDS-PAGE corresponding to these SEC-MALS traces, because unfortunately our SEC-MALS instrument is not equipped with a fraction collector. Reviewer #2: The enzyme poly(ADP-ribose) polymerase-1 (PARP1), and the related enzyme PARP2, promote single- and double-strand DNA break repair in cells, by facilitating the local remodeling of chromatin into a repair-permissive configuration. PARP inhibitors suppress the repair of DNA damaged by radio- or chemotherapy, making them valuable in cancer therapy. This naturally has spurred efforts to better understand how the PARP enzymes function in chromatin. This manuscript presents the first cryo-EM structure of PARP2 bound to a DNA end near the edge of a nucleosome. The data throughout appear very solid, the interpretations are consistent with previous studies of PARP-2 structure and function, and the methods are clearly and thoroughly described. As such, I think this study will meaningfully advance the field. My only substantive comment relates to how PARP2 drives formation of the ‘di-nucleosomes’ used for structural analyses. At appropriate concentrations, the capacity of PARP2 to dimerize drove formation of di-nucleosomes, in which two PARP-2 molecules serve to bridge the DNA ends of two previously separate nucleosomes. The resulting complex (i.e. one PARP2 dimer and two nucleosomes) appears surprisingly homogeneous, as if the two nucleosomes were rotationally constrained relative to one another. One is tempted to attribute this homogeneity to the PARP2 dimer but, as the authors note, they cannot rule out stabilization through interactions between histone tails in one nucleosome and DNA in the adjacent nucleosome. Unfortunately, only the WGR-domain of PARP2 was amenable to structural analyses in this study. Previous X-ray crystallographic studies (PMID: 30321391) indicate that the WGR domain interacts with a 5’-phosphate at the break. However, that domain does not mediate dimer formation. Thus, while it seems highly likely that PARP2 contributes to di-nucleosome formation, it remains unclear if inter-nucleosome interactions between histones and DNA contribute as well. If such interactions occur, they would presumably be suppressed by the acetylation of histone tails in the model nucleosomes. Knowing how back-breakingly laborious cryo-EM studies can be, I don’t see this control experiment as obligatory but, ultimately, it might prove worthwhile. In the previously published crystal structure of the WGR of PARP2 bound to DNA (PDB 6F5B, PMID 30321391, each copy of the WGR domain makes protein-DNA interactions not only with the 5’-phosphate at the break site, but also with DNA strands on both sides of the break, while the two WGR domains are too far apart to make protein-protein interactions between each other. What drives DNA bridging is therefore not a propensity of PARP2 to dimerize (it is monomeric in the absence of DNA, as we determined by SEC-MALS in figure S2A, in agreement with PMID 30321391), but the specific binding of its WGR domain to DNA ends. Our cryo-EM map is fully consistent with the conformation of the WGR domain and bridged DNA dimer present in PDB 6F5B. We speculate that the basic N-terminal region of PARP2 provides further binding affinity for DNA and could stabilize the bridged nucleosome dimer, but the resolution of our cryo-EM map is not sufficient to either support or reject this hypothesis. We appreciate the reviewer’s understanding of the amount of work that went into this cryo-EM study, and confirm that repeating it with chemically acetylated histone tails is not reasonably feasible in the timeframe we are allowed for the revisions. Additionally, in light of the recent publication from the Ahel / Matic lab (PMID 32939087) that was released last week, this is not warranted. Attachments Attachment Submitted filename: response-v1.docx https://doi.org/10.1371/journal.pone.0240932.r002
6 Oct 2020 Decision Letter - Robert W Sobol, Editor Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1 PONE-D-20-24696R1 Dear Dr. Luger, It was a pleasure to read this paper. We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Robert W Sobol, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors have addressed all the concerns raised during the review process. No further comments at this time. Reviewer #2: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No https://doi.org/10.1371/journal.pone.0240932.r003
Formally Accepted
12 Oct 2020 Acceptance Letter - Robert W Sobol, Editor PONE-D-20-24696R1 Bridging of nucleosome-proximal DNA double-strand breaks by PARP2 enhances its interaction with HPF1 Dear Dr. Luger: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Robert W Sobol Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0240932.r004

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